Resistance gene–guided genome mining reveals the roseopurpurins as inhibitors of cyclin-dependent kinases

Abstract

With the significant increase in the availability of microbial genome sequences in recent years, resistance gene-guided genome mining has emerged as a powerful approach for identifying natural products with specific bioactivities. Here, we present the use of this approach to reveal the roseopurpurins as potent inhibitors of cyclin-dependent kinases (CDKs), a class of cell cycle regulators implicated in multiple cancers. We identified a biosynthetic gene cluster (BGC) with a putative resistance gene with homology to human CDK2. Using targeted gene disruption and transcription factor overexpression in <i>Aspergillus uvarum</i>, and heterologous expression of the BGC in <i>Aspergillus nidulans,</i> we demonstrated that roseopurpurin C (<b>1</b>) is produced by this cluster and characterized its biosynthesis. We determined the potency, specificity, and mechanism of action of <b>1</b> as well as multiple intermediates and shunt products produced from the BGC. We show that <b>1</b> inhibits human CDK2 with a <i>K</i>_iapp of 44 nM, demonstrates selectivity for clinically relevant members of the CDK family, and induces G1 cell cycle arrest in HCT116 cells. Structural analysis of <b>1</b> complexed with CDK2 revealed the molecular basis of ATP-competitive inhibition.